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Plot tweaks to make paper quality #576

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merged 19 commits into from
Dec 23, 2020
Merged

Plot tweaks to make paper quality #576

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f009429
added reliability comparison plots and twinning mean profile plots
36000 Oct 19, 2020
775c89f
add profile reliability comparison capability
36000 Oct 19, 2020
ba31572
tweaking rel comparison plots
36000 Oct 19, 2020
7a3e067
bug fix
36000 Oct 20, 2020
5947067
have option to remove model for scalar in group csv comparison
36000 Oct 27, 2020
1b2347d
marker size
36000 Nov 2, 2020
296ca63
customize rel plot axes label
36000 Nov 2, 2020
9c9157b
color axis in twinning plots
36000 Nov 2, 2020
bf277b9
add fishers transformation; tweak more font sizes
36000 Nov 6, 2020
d1a61b9
many rel plot tweaks
36000 Nov 12, 2020
3327de2
fix rotation
36000 Nov 12, 2020
2f1a1b8
more tweaks; make more things bundly colorful
36000 Nov 19, 2020
9636307
more plotting tweaks
36000 Nov 30, 2020
8d9dd72
integrate recobundles
36000 Dec 2, 2020
434fd58
tweak plots; fix cbv bug
36000 Dec 3, 2020
54f6fe8
make remove_model default
36000 Dec 7, 2020
e88266a
more versatile mAFQ conversion
36000 Dec 11, 2020
bc1d61c
pep8
36000 Dec 22, 2020
c034312
doc typo
36000 Dec 22, 2020
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8 changes: 8 additions & 0 deletions AFQ/api.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1542,6 +1542,7 @@ def _viz_bundles(self, row,
color_by_volume=None,
cbv_lims=[None, None],
xform_color_by_volume=False,
volume_opacity=0.3,
n_points=40):
bundles_file = self._clean_bundles(row)

Expand All @@ -1555,6 +1556,7 @@ def _viz_bundles(self, row,
)

figure = self.viz.visualize_volume(volume,
opacity=volume_opacity,
interact=False,
inline=False)

Expand Down Expand Up @@ -1598,6 +1600,7 @@ def _viz_ROIs(self, row,
color_by_volume=None,
cbv_lims=[None, None],
xform_color_by_volume=False,
volume_opacity=0.3,
n_points=40):
bundles_file = self._clean_bundles(row)

Expand All @@ -1617,6 +1620,7 @@ def _viz_ROIs(self, row,
self.logger.info(f"Generating {bundle_name} visualization...")
uid = self.bundle_dict[bundle_name]['uid']
figure = self.viz.visualize_volume(volume,
opacity=volume_opacity,
interact=False,
inline=False)
try:
Expand Down Expand Up @@ -1996,6 +2000,7 @@ def viz_bundles(self,
color_by_volume=None,
cbv_lims=[None, None],
xform_color_by_volume=False,
volume_opacity=0.3,
n_points=40,
inline=False,
interactive=False):
Expand All @@ -2007,6 +2012,7 @@ def viz_bundles(self,
color_by_volume=color_by_volume,
cbv_lims=cbv_lims,
xform_color_by_volume=xform_color_by_volume,
volume_opacity=volume_opacity,
n_points=n_points,
inline=inline,
interactive=interactive)
Expand All @@ -2019,6 +2025,7 @@ def viz_ROIs(self,
color_by_volume=None,
cbv_lims=[None, None],
xform_color_by_volume=False,
volume_opacity=0.3,
n_points=40,
inline=False,
interactive=False):
Expand All @@ -2034,6 +2041,7 @@ def viz_ROIs(self,
color_by_volume=color_by_volume,
cbv_lims=cbv_lims,
xform_color_by_volume=xform_color_by_volume,
volume_opacity=volume_opacity,
n_points=n_points)

def plot_tract_profiles(self):
Expand Down
15 changes: 14 additions & 1 deletion AFQ/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,20 +68,33 @@
"UF_L": "UNC_L", "UF_R": "UNC_R",
"IFOF_L": "IFO_L", "IFOF_R": "IFO_R",
"CST_L": "CST_L", "CST_R": "CST_R",
"ILF_L": "ILF_L", "ILF_R": "ILF_R",
"SLF_L": "SLF_L", "SLF_R": "SLF_R"
}

BUNDLE_MAT_2_PYTHON = \
{'Right Corticospinal': 'CST_R', 'Left Corticospinal': 'CST_L',
'RightCorticospinal': 'CST_R', 'LeftCorticospinal': 'CST_L',
'Right Uncinate': 'UNC_R', 'Left Uncinate': 'UNC_L',
'RightUncinate': 'UNC_R', 'LeftUncinate': 'UNC_L',
'Left IFOF': 'IFO_L', 'Right IFOF': 'IFO_R',
'LeftIFOF': 'IFO_L', 'RightIFOF': 'IFO_R',
'Right Arcuate': 'ARC_R', 'Left Arcuate': 'ARC_L',
'RightArcuate': 'ARC_R', 'LeftArcuate': 'ARC_L',
'Right Thalamic Radiation': 'ATR_R', 'Left Thalamic Radiation': 'ATR_L',
'RightThalamicRadiation': 'ATR_R', 'LeftThalamicRadiation': 'ATR_L',
'Right Cingulum Cingulate': 'CGC_R', 'Left Cingulum Cingulate': 'CGC_L',
'RightCingulumCingulate': 'CGC_R', 'LeftCingulumCingulate': 'CGC_L',
'Right Cingulum Hippocampus': 'HCC_R',
'Left Cingulum Hippocampus': 'HCC_L',
'RightCingulumHippocampus': 'HCC_R',
'LeftCingulumHippocampus': 'HCC_L',
'Callosum Forceps Major': 'FP', 'Callosum Forceps Minor': 'FA',
'CallosumForcepsMajor': 'FP', 'CallosumForcepsMinor': 'FA',
'Right ILF': 'ILF_R', 'Left ILF': 'ILF_L',
'Right SLF': 'SLF_R', 'Left SLF': 'SLF_L'}
'RightILF': 'ILF_R', 'LeftILF': 'ILF_L',
'Right SLF': 'SLF_R', 'Left SLF': 'SLF_L',
'RightSLF': 'SLF_R', 'LeftSLF': 'SLF_L'}

afq_home = op.join(op.expanduser('~'), 'AFQ_data')

Expand Down
10 changes: 5 additions & 5 deletions AFQ/viz/plotly_backend.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,12 +81,12 @@ def _draw_streamlines(figure, sls, dimensions, color, name, cbv=None,
y_pts = np.zeros(plotting_shape)
z_pts = np.zeros(plotting_shape)

if cbv_lims[0] is None:
cbv_lims[0] = 0
if cbv_lims[1] is None:
cbv_lims[1] = cbv.max()

if cbv is not None:
if cbv_lims[0] is None:
cbv_lims[0] = 0
if cbv_lims[1] is None:
cbv_lims[1] = cbv.max()

customdata = np.zeros(plotting_shape)
line_color = np.zeros((plotting_shape, 3))
color_constant = (color / color.max())\
Expand Down
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